* using log directory 'd:/RCompile/CRANincoming/R-devel/circlize.Rcheck' * using R version 4.6.0 alpha (2026-04-02 r89777 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-04-03 08:45:35 UTC * checking for file 'circlize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'circlize' version '0.4.18' * checking CRAN incoming feasibility ... [13s] NOTE Maintainer: 'Zuguang Gu ' New maintainer: Zuguang Gu Old maintainer(s): Zuguang Gu Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: http://circos.ca/intro/tabular_visualization/ (moved to https://circos.ca/intro/tabular_visualization/) From: man/chordDiagram.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'circlize' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: 'CODE_OF_CONDUCT.md' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: 'spiralize' Unexported object imported by a ':::' call: 'spiralize:::construct_dend_segments' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [34s] NOTE circos.initialize: no visible global function definition for 'grid.newpage' circos.initialize: no visible global function definition for 'pushViewport' circos.initialize: no visible global function definition for 'viewport' circos.initialize: no visible global function definition for 'grid.layout' Undefined global functions or variables: grid.layout grid.newpage pushViewport viewport * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'circos.genomicDensity.Rd': circos.genomicDensity Code: function(data, ylim.force = FALSE, window.size = NULL, overlap = TRUE, count_by = c("percent", "number"), col = ifelse(area, "grey", "black"), lwd = par("lwd"), lty = par("lty"), type = "l", area = TRUE, area.baseline = NULL, baseline = 0, border = NA, use_horizon = FALSE, horizon_param = list(), ...) Docs: function(data, ylim.force = FALSE, window.size = NULL, overlap = TRUE, count_by = c("percent", "number"), col = ifelse(area, "grey", "black"), lwd = par("lwd"), lty = par("lty"), type = "l", area = TRUE, area.baseline = NULL, baseline = 0, border = NA, ...) Argument names in code not in docs: use_horizon horizon_param Mismatches in argument names: Position: 14 Code: use_horizon Docs: ... Codoc mismatches from Rd file 'circos.initialize.Rd': circos.initialize Code: function(sectors = NULL, x = NULL, xlim = NULL, sector.width = NULL, offset = NULL, factors = sectors, ring = FALSE, newpage = TRUE) Docs: function(sectors = NULL, x = NULL, xlim = NULL, sector.width = NULL, factors = sectors, ring = FALSE) Argument names in code not in docs: offset newpage Mismatches in argument names: Position: 5 Code: offset Docs: factors Position: 6 Code: factors Docs: ring Codoc mismatches from Rd file 'circos.trackPlotRegion.Rd': circos.trackPlotRegion Code: function(sectors = NULL, x = NULL, y = NULL, ylim = NULL, force.ylim = TRUE, track.index = NULL, track.height = circos.par("track.height"), track.margin = circos.par("track.margin"), cell.padding = circos.par("cell.padding"), bg.col = NA, bg.border = "black", bg.lty = par("lty"), bg.lwd = par("lwd"), panel.fun = function(x, y) { NULL}, radius = NULL, offset = NULL, factors = sectors) Docs: function(sectors = NULL, x = NULL, y = NULL, ylim = NULL, force.ylim = TRUE, track.index = NULL, track.height = circos.par("track.height"), track.margin = circos.par("track.margin"), cell.padding = circos.par("cell.padding"), bg.col = NA, bg.border = "black", bg.lty = par("lty"), bg.lwd = par("lwd"), panel.fun = function(x, y) { NULL}, radius = NULL, factors = sectors) Argument names in code not in docs: offset Mismatches in argument names: Position: 16 Code: offset Docs: factors * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'circlize-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CELL_META > ### Title: Easy way to get meta data in the current cell > ### Aliases: CELL_META > > ### ** Examples > > pdf(NULL) > circos.initialize("a", xlim = c(0, 1)) Error in grid.newpage() : could not find function "grid.newpage" Calls: circos.initialize Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... NOTE Package vignette with \VignetteEngine{} not specifying an engine package: 'circlize.Rmd' Engines should be specified as \VignetteEngine{PKG::ENG}. * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [33s] OK * checking HTML version of manual ... [32s] OK * DONE Status: 1 ERROR, 2 WARNINGs, 4 NOTEs